Exploring RNA folding one molecule at a time

Technological advancements in deciphering RNA-RNA interactions

RNA-RNA interactions (RRIs) can dictate RNA molecules to form intricate higher-order structures and bind their RNA substrates in diverse biological processes. To elucidate the function, binding specificity, and regulatory mechanisms of various RNA molecules, especially the vast repertoire of non-coding RNAs, advanced technologies and methods that globally map RRIs are extremely valuable. In the past decades, many state-of-the-art technologies have been developed for this purpose. This review focuses on those high-throughput technologies for the global mapping of RRIs. We summarize the key concepts and the pros and cons of different technologies. In addition, we highlight the novel biological insights uncovered by these RRI mapping methods and discuss the future challenges for appreciating the crucial roles of RRIs in gene regulation across bacteria, viruses, archaea, and mammals.

Measurement of the specific and non-specific binding energies of Mg2+ to RNA

Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.

Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level

Measurements of the thermodynamic properties of biomolecular folding (ΔG°, ΔH°, ΔS°, etc.) provide a wealth of information on the folding process and have long played a central role in biophysical investigation. In particular, the excess heat capacity of folding (ΔC_P) is crucial, as typically measured in bulk ensemble studies by differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). Here, we report the first measurements of ΔC_P at the single-molecule level using the single-molecule fluorescence resonance energy transfer (smFRET) as well as the very first measurements of the heat capacity change associated with achieving the transition state (ΔC^‡_P) for nucleic acid folding. The deoxyribonucleic acid (DNA) hairpin used in these studies exhibits an excess heat capacity for hybridization (ΔC_P = -340 ± 60 J/mol/K per base pair) consistent with the range of literature expectations (ΔC_P = -100 to -420 J/mol/K per base pair). Furthermore, the measured activation heat capacities (ΔC^‡_P) for such hairpin unfolding are consistent with a folding transition state containing few fully formed base pairs, in agreement with prevailing models of DNA hybridization.

Solid-State NMR Study to Probe the Effects of Divalent Metal Ions (Ca2+ and Mg2+) on the Magnetic Alignment of Polymer-Based Lipid Nanodiscs

Divalent cations, especially Ca2+ and Mg2+, play a vital role in the function of biomolecules and making them important to be constituents in samples for in vitro biophysical and biochemical characterizations. Although lipid nanodiscs are becoming valuable tools for structural biology studies on membrane proteins and for drug delivery, most types of nanodiscs used in these studies are unstable in the presence of divalent metal ions. To avoid the interaction of divalent metal ions with the belt of the nanodiscs, synthetic polymers have been designed and demonstrated to form stable lipid nanodiscs under such unstable conditions. Such polymer-based nanodiscs have been shown to provide an ideal platform for structural studies using both solid-state and solution NMR spectroscopies because of the near-native cell-membrane environment they provide and the unique magnetic-alignment behavior of large-size nanodiscs. In this study, we report an investigation probing the effects of Ca2+ and Mg2+ ions on the formation of polymer-based lipid nanodiscs and the magnetic-alignment properties using a synthetic polymer, styrene maleimide quaternary ammonium (SMA-QA), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids. Phosphorus-31 NMR experiments were used to evaluate the stability of the magnetic-alignment behavior of the nanodiscs for varying concentrations of Ca2+ or Mg2+ at different temperatures. It is remarkable that the interaction of divalent cations with lipid headgroups promotes the stacking up of nanodiscs that results in the enhanced magnetic alignment of nanodiscs. Interestingly, the reported results show that both the temperature and the concentration of divalent metal ions can be optimized to achieve the optimal alignment of nanodiscs in the presence of an applied magnetic field. We expect the reported results to be useful in the design of nanodisc-based nanoparticles for various applications in addition to atomic-resolution structural and dynamics studies using NMR and other biophysical techniques.

Pushing Camera-Based Single-Molecule Kinetic Measurements to the Frame Acquisition Limit with Stroboscopic smFRET

Single-molecule fluorescence resonance energy transfer (smFRET) experiments permit detailed examination of microscopic dynamics. However, kinetic rate constants determined by smFRET are susceptible to systematic underestimation when the rate constants are comparable to the data acquisition rate. We demonstrate how such systematic errors in camera-based total internal reflection fluorescence microscopy experiments can be greatly reduced by using stroboscopic illumination/detection, allowing accurate rate constant determination up to the data sampling rate and yielding an order of magnitude increase in the dynamic range. Implementation of these stroboscopic smFRET ideas is straightforward, and the stroboscopically obtained data are compatible with multiple trajectory analysis methods, including dwell-time analysis and hidden Markov modeling. Such stroboscopic methods therefore offer a remarkably simple yet valuable addition to the smFRET toolkit, requiring only relatively modest modification to the normal data collection and analysis procedures.

Cooperativity and Allostery in RNA Systems

Allostery is among the most basic biological principles employed by biological macromolecules to achieve a biologically active state in response to chemical cues. Although initially used to describe the impact of small molecules on the conformation and activity of protein enzymes, the definition of this term has been significantly broadened to describe long-range conformational change of macromolecules in response to small or large effectors. Such a broad definition could be applied to RNA molecules, which do not typically serve as protein-free cellular enzymes but fold and form macromolecular assemblies with the help of various ligand molecules, including ions and proteins. Ligand-induced allosteric changes in RNA molecules are often accompanied by cooperative interactions between RNA and its ligand, thus streamlining the folding and assembly pathways. This chapter provides an overview of the interplay between cooperativity and allostery in RNA systems and outlines methods to study these two biological principles.

Large Phenotypic Enhancement of Structured Random RNA Pools

Laboratory evolution of functional RNAs has applications in many areas of chemical and synthetic biology. In vitro selections critically depend on the presence of functional molecules, such as aptamers and ribozymes, in the starting sequence pools. For selection of novel functions the pools are typically transcribed from random-sequence DNA templates, yielding a highly diverse set of RNAs that contain a multitude of folds and biochemical activities. The phenotypic potential, the frequency of functional RNAs, is very low, requiring large complexity of starting pools, surpassing 10¹⁵ different sequences, to identify highly active isolates. Furthermore, the majority of random sequences is not structured and has a high propensity for aggregation; the in vitro selection process thus involves not just enrichment of functional RNAs, but also their purification from aggregation-prone "free-riders". We reasoned that purification of the nonaggregating, monomeric subpopulation of a random-sequence RNA pool will yield pools of folded, functional RNAs. We performed six rounds of selection for monomeric sequences and show that the enriched population is compactly folded. In vitro selections originating from various mixtures of the compact pool and a fully random pool showed that sequences from the compact pool always dominate the population once a biochemical activity is detectable. A head-to-head competition of the two pools starting from a low (5 × 10¹²) sequence diversity revealed that the phenotypic potential of the compact pool is about 1000-times higher than the fully random pool. A selection for folded and monomeric RNA pools thus greatly increases the frequency of functional RNAs from that seen in random-sequence pools, providing a facile experimental approach to isolation of highly active functional RNAs from low-diversity populations.

Structural Biology outside the box-inside the cell

Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg(2+) or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways.

N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding

N(6)-Methyladenosine (m(6)A) is a reversible and abundant internal modification of messenger RNA (mRNA) and long noncoding RNA (lncRNA) with roles in RNA processing, transport, and stability. Although m(6)A does not preclude Watson-Crick base pairing, the N(6)-methyl group alters the stability of RNA secondary structure. Since changes in RNA structure can affect diverse cellular processes, the influence of m(6)A on mRNA and lncRNA structure has the potential to be an important mechanism for m(6)A function in the cell. Indeed, an m(6)A site in the lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was recently shown to induce a local change in structure that increases the accessibility of a U5-tract for recognition and binding by heterogeneous nuclear ribonucleoprotein C (HNRNPC). This m(6)A-dependent regulation of protein binding through a change in RNA structure, termed "m(6)A-switch", affects transcriptome-wide mRNA abundance and alternative splicing. To further characterize this first example of an m(6)A-switch in a cellular RNA, we used nuclear magnetic resonance and Förster resonance energy transfer to demonstrate the effect of m(6)A on a 32-nucleotide RNA hairpin derived from the m(6)A-switch in MALAT1. The observed imino proton nuclear magnetic resonance resonances and Förster resonance energy transfer efficiencies suggest that m(6)A selectively destabilizes the portion of the hairpin stem where the U5-tract is located, increasing the solvent accessibility of the neighboring bases while maintaining the overall hairpin structure. The m(6)A-modified hairpin has a predisposed conformation that resembles the hairpin conformation in the RNA-HNRNPC complex more closely than the unmodified hairpin. The m(6)A-induced structural changes in the MALAT1 hairpin can serve as a model for a large family of m(6)A-switches that mediate the influence of m(6)A on cellular processes.

Native purification and labeling of RNA for single molecule fluorescence studies

The recent discovery that non-coding RNAs are considerably more abundant and serve a much wider range of critical cellular functions than recognized over previous decades of research into molecular biology has sparked a renewed interest in the study of structure-function relationships of RNA. To perform their functions in the cell, RNAs must dominantly adopt their native conformations, avoiding deep, non-productive kinetic traps that may exist along a frustrated (rugged) folding free energy landscape. Intracellularly, RNAs are synthesized by RNA polymerase and fold co-transcriptionally starting from the 5' end, sometimes with the aid of protein chaperones. By contrast, in the laboratory RNAs are commonly generated by in vitro transcription or chemical synthesis, followed by purification in a manner that includes the use of high concentrations of urea, heat and UV light (for detection), resulting in the denaturation and subsequent refolding of the entire RNA. Recent studies into the nature of heterogeneous RNA populations resulting from this process have underscored the need for non-denaturing (native) purification methods that maintain the co-transcriptional fold of an RNA. Here, we present protocols for the native purification of an RNA after its in vitro transcription and for fluorophore and biotin labeling methods designed to preserve its native conformation for use in single molecule fluorescence resonance energy transfer (smFRET) inquiries into its structure and function. Finally, we present methods for taking smFRET data and for analyzing them, as well as a description of plausible overall preparation schemes for the plethora of non-coding RNAs.

Single-molecule fluorescence-based studies on the dynamics, assembly and catalytic mechanism of the spliceosome

Pre-mRNA (precursor mRNA) splicing is a key step in cellular gene expression where introns are excised and exons are ligated together to produce mature mRNA. This process is catalysed by the spliceosome, which consists of five snRNPs (small nuclear ribonucleoprotein particles) and numerous protein factors. Assembly of these snRNPs and associated proteins is a highly dynamic process, making it challenging to study the conformational rearrangements and spliceosome assembly kinetics in bulk studies. In the present review, we discuss recent studies utilizing techniques based on single-molecule detection that have helped overcome this challenge. These studies focus on the assembly dynamics and splicing kinetics in real-time, which help understanding of spliceosomal assembly and catalysis.

Memory-efficient RNA energy landscape exploration

MOTIVATION

Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches.

RESULTS

We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes.

AVAILABILITY AND IMPLEMENTATION

Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/.

RNA folding dynamics using laser-assisted single-molecule refolding

RNA folding pathways can be complex and even include kinetic traps or misfolded intermediates that can be slow to resolve. Characterizing these pathways is critical to understanding how RNA molecules acquire their biological function. We have previously developed a novel approach to help characterize such misfolded intermediates. Laser-assisted single-molecule refolding (LASR) is a powerful technique that combines temperature-jump (T-jump) kinetics with single-molecule detection. In a typical LASR experiment, the temperature is rapidly increased and conformational dynamics are characterized, in real-time, at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide detailed protocols for performing LASR experiments including sample preparation, temperature calibration, and data analysis.

Ultrastable atomic force microscopy: improved force and positional stability

Atomic force microscopy (AFM) is an exciting technique for biophysical studies of single molecules, but its usefulness is limited by instrumental drift. We dramatically reduced positional drift by adding two lasers to track and thereby actively stabilize the tip and the surface. These lasers also enabled label-free optical images that were spatially aligned to the tip position. Finally, sub-pN force stability over 100 s was achieved by removing the gold coating from soft cantilevers. These enhancements to AFM instrumentation can immediately benefit research in biophysics and nanoscience.

Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics

The ribonucleoprotein telomerase is an RNA-dependent DNA polymerase that catalyzes the repetitive addition of a short, species-specific, DNA sequence to the ends of linear eukaryotic chromosomes. The single RNA component of telomerase contains both the template sequence for DNA synthesis and a functionally critical pseudoknot motif, which can also exist as a less stable hairpin. Here we use a minimal version of the human telomerase RNA pseudoknot to study this hairpin-pseudoknot structural equilibrium using temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) experiments. The urea dependence of these experiments aids in determination of the folding kinetics and thermodynamics. The wild-type pseudoknot behavior is compared and contrasted to a mutant pseudoknot sequence implicated in a genetic disorder-dyskeratosis congenita. These findings clearly identify that this 2nt noncomplementary mutation destabilizes the folding of the wild-type pseudoknot by substantially reducing the folding rate constant (≈ 400-fold) while only nominally increasing the unfolding rate constant (≈ 5-fold). Furthermore, the urea dependence of the equilibrium and rate constants is used to develop a free energy landscape for this unimolecular equilibrium and propose details about the structure of the transition state. Finally, the urea-dependent folding experiments provide valuable physical insights into the mechanism for destabilization of RNA pseudoknots by such chemical denaturants.

Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex

The spliceosome catalyzes precursor-mRNA splicing in all eukaryotes. It consists of over 100 proteins and five small nuclear RNAs (snRNAs), including U2 and U6 snRNAs, which are essential for catalysis. Human and yeast snRNAs share structural similarities despite the fact that human snRNAs contain numerous post-transcriptional modifications. Although functions for these modifications have been proposed, their exact roles are still not well understood. To help elucidate these roles in pre-mRNA splicing, we have used single-molecule fluorescence to characterize the effect of several post-transcriptional modifications in U2 snRNA on the conformation and dynamics of the U2-U6 complex in vitro. Consistent with yeast, the human U2-U6 complex reveals the presence of a magnesium-dependent dynamic equilibrium among three conformations. Interestingly, our data show that modifications in human U2 stem I modulate the dynamic equilibrium of the U2-U6 complex by stabilizing the four-helix structure. However, the small magnitude of this effect suggests that post-transcriptional modifications in human snRNAs may have a primary role in the mediation of specific RNA-protein interactions in vivo.

Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg(II) and Ag(I) ions

The metal-induced folding of thymine-cytosine-rich oligonucleotides into hairpin-like structures was characterised by isothermal titration calorimetry, secondary structure analysis, equilibrium titrations, and fluorescence study. We find that designed thymine-cytosine-rich oligonucleotides can specifically bind with Hg(II) or Ag(I) ions to generate metal-mediated base pairs in a hairpin-like structure from a random coil structure. Isothermal titration calorimetry experiments were performed to reveal the detail of the whole binding process. The thermodynamic result exhibits two possible pathways of significant change upon the addition of Hg(II) ions. Furthermore, this transformation can be enhanced by the presence of Ag(I) ions. The fluorescence decreases through fluorescence resonance energy transfer (FRET) between the fluorophore and quencher confirms the process of formation of the hairpin-like structure. The analysis of optical titration data demonstrates that the saturated binding stoichiometries are 12:1 and 4:1 for Hg(II) and Ag(I) ions, respectively. Our result provides a promising strategy for the investigation of the mechanism of structural transformation of oligonucleotides influenced by metal-mediated base pairs, which may eventually lead to progress in constructing a metal-triggered DNA origami system and metal-containing DNA nanotechnology.

Effect of divalent cations on DMPC/DHPC bicelle formation and alignment

Many important classes of biomolecules require divalent cations for optimal activity, making these ions essential for biologically relevant structural studies. Bicelle mixtures composed of short-chain and long-chain lipids are often used in solution- and solid-state NMR structure determination; however, the phase diagrams of these useful orienting media and membrane mimetics are sensitive to other solution components. Therefore, we have investigated the effect of varying concentrations of four divalent cations, Ca(2+), Mg(2+), Zn(2+), and Cd(2+), on cholesterol sulfate-stabilized DMPC/DHPC bicelles. We found that low concentrations of all the divalent ions are tolerated with minimal perturbation. At higher concentrations Zn(2+) and Cd(2+) disrupt the magnetically aligned phase while Ca(2+) and Mg(2+) produce more strongly oriented phases. This result indicates that divalent cations are not only required to maintain the biological activity of proteins and nucleic acids; they may also be used to manipulate the behavior of the magnetically aligned phase.

Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding

Cyclic diguanylate (c-di-GMP) is a bacterial second messenger important for physiologic adaptation and virulence. Class-I c-di-GMP riboswitches are phylogenetically widespread and thought to mediate pleiotropic genetic responses to the second messenger. Previous studies suggest that the RNA aptamer domain switches from an extended free state to a compact, c-di-GMP-bound conformation in which two helical stacks dock side-by-side. Single molecule fluorescence resonance energy transfer (smFRET) experiments now reveal that the free RNA exists in four distinct populations that differ in dynamics in the extended and docked conformations. In the presence of c-di-GMP and Mg(2+), a stably docked population (>30 min) becomes predominant. smFRET mutant analysis demonstrates that tertiary interactions distal to the c-di-GMP binding site strongly modulate the RNA population structure, even in the absence of c-di-GMP. These allosteric interactions accelerate ligand recognition by preorganizing the RNA, favoring rapid c-di-GMP binding.

Thermodynamic origins of monovalent facilitated RNA folding

Cations have long been associated with formation of native RNA structure and are commonly thought to stabilize the formation of tertiary contacts by favorably interacting with the electrostatic potential of the RNA, giving rise to an "ion atmosphere". A significant amount of information regarding the thermodynamics of structural transitions in the presence of an ion atmosphere has accumulated and suggests stabilization is dominated by entropic terms. This work provides an analysis of how RNA-cation interactions affect the entropy and enthalpy associated with an RNA tertiary transition. Specifically, temperature-dependent single-molecule fluorescence resonance energy transfer studies have been exploited to determine the free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) of folding for an isolated tetraloop-receptor tertiary interaction as a function of Na(+) concentration. Somewhat unexpectedly, increasing the Na(+) concentration changes the folding enthalpy from a strongly exothermic process [e.g., ΔH° = -26(2) kcal/mol at 180 mM] to a weakly exothermic process [e.g., ΔH° = -4(1) kcal/mol at 630 mM]. As a direct corollary, it is the strong increase in folding entropy [Δ(ΔS°) > 0] that compensates for this loss of exothermicity for the achievement of more favorable folding [Δ(ΔG°) < 0] at higher Na(+) concentrations. In conjunction with corresponding measurements of the thermodynamics of the transition state barrier, these data provide a detailed description of the folding pathway associated with the GAAA tetraloop-receptor interaction as a function of Na(+) concentration. The results support a potentially universal mechanism for monovalent facilitated RNA folding, whereby an increasing monovalent concentration stabilizes tertiary structure by reducing the entropic penalty for folding.

Analysis of RNA folding and ribonucleoprotein assembly by single-molecule fluorescence spectroscopy

To execute their diverse range of biological functions, RNA molecules must fold into specific tertiary structures and/or associate with one or more proteins to form ribonucleoprotein (RNP) complexes. Single-molecule fluorescence spectroscopy is a powerful tool for the study of RNA folding and RNP assembly processes, directly revealing different conformational subpopulations that are hidden in conventional ensemble measurements. Moreover, kinetic processes can be observed without the need to synchronize a population of molecules. In this chapter, we describe the fluorescence spectroscopic methods used for single-molecule measurements of freely diffusing or immobilized RNA molecules or RNA-protein complexes. We also provide practical protocols to prepare the fluorescently labeled RNA and protein molecules required for such studies. Finally, we provide two examples of how these various preparative and spectroscopic methods are employed in the study of RNA folding and RNP assembly processes.

Single molecule FRET characterization of large ribozyme folding

A procedure to investigate the folding of group II intron by single molecule Fluorescence Resonance Energy Transfer (smFRET) using total internal reflection fluorescence microscopy (TIRFM) is described in this chapter. Using our previous studies on the folding and dynamics of a large ribozyme in the presence of metal ions (i.e., Mg(2+) and Ca(2+)) and/or the DEAD-box protein Mss116 as an example, we here describe step-by-step procedures to perform experiments. smFRET allows the investigation of individual molecules, thus, providing kinetic and mechanistic information hidden in ensemble averaged experiments.

A microsecond microfluidic mixer for characterizing fast biochemical reactions

Analysis of fast biochemical reactions requires rapid mixing of solutions. Micromixers can achieve uniform mixing of solutions in a short time and have been recognized as an attractive tool to analyze fast reactions. However, it is still a challenge to design mixers with simple structure and short dead time. Here, a zigzag turbulent micromixer was developed with a rapid mixing time of 16 μs at sample consumption of 10 μL/s. Numerical simulations and confocal imaging validated this result. Application of the chemiluminescence (CL) reaction demonstrated the use of this mixer in analyzing the kinetic process of the CL reaction. In comparison to the turbulent micromixers reported previously, this zigzag mixer has advantages of short dead time, simple structure and low sample consumption. We anticipate the developed mixer to be a useful tool in studying biochemical kinetics or be integrated to Lab-on-a-chip device as a pretreatment functional unit.

Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA

Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag(+) ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag(+) ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag(+) ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 10(6) M(-1) binding constant, which was significantly larger than those for nonspecific metal ion-DNA interactions. The specific binding between the Ag(+) ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag(+) ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag(+) binding. The binding affinity for the second Ag(+) binding was similar to that for the first Ag(+) binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag(+) ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.

RNA dynamics: perspectives from spin labels

Dynamics are important and indispensible physical attributes that play essential roles in RNA function. RNA dynamics are complex, spanning vast timescales, and encompassing a large number of physical modes. The technique of site-directed spin labeling (SDSL), which derives information on local structural and dynamic features of a macromolecule by monitoring a chemically stable nitroxide radical using electron paramagnetic resonance spectroscopy, has been applied to monitor intrinsic dynamics at defined structural states as well as to probe conformational transition dynamics of RNAs. The current state of SDSL studies of RNA dynamics is summarized here. Further development and application of SDSL promise to open up many more opportunities for probing RNA dynamics and connecting dynamics to structure and function.

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA

Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick base pair opening which is not consistent with experiment, whereas analysis of molecular dynamics (MD) simulations show the 2'-hydroxyl moiety to almost exclusively sample the O3' orientation. Quantum mechanical (QM) studies of RNA related model compounds indicate the energy minimum associated with the O3' orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2'-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3' orientations of the 2'-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2'-hydroxyl moiety and support a model whereby the 2'-hydroxyl can enhance the probability of conformational transitions in RNA.

Conformational capture of the SAM-II riboswitch

Riboswitches are gene regulation elements in mRNA that function by specifically responding to metabolites. Although the metabolite-bound states of riboswitches have proven amenable to structure determination efforts, knowledge of the structural features of riboswitches in their ligand-free forms and their ligand-response mechanisms giving rise to regulatory control is lacking. Here we explore the ligand-induced folding process of the S-adenosylmethionine type II (SAM-II) riboswitch using chemical and biophysical methods, including NMR and fluorescence spectroscopy, and single-molecule fluorescence imaging. The data reveal that the unliganded SAM-II riboswitch is dynamic in nature, in that its stem-loop element becomes engaged in a pseudoknot fold through base-pairing with nucleosides in the 3' overhang containing the Shine-Dalgarno sequence. Although the pseudoknot structure is highly transient in the absence of its ligand, S-adenosylmethionine (SAM), it becomes conformationally restrained upon ligand recognition, through a conformational capture mechanism. These insights provide a molecular understanding of riboswitch dynamics that shed new light on the mechanism of riboswitch-mediated translational regulation.

Enhancement of single-molecule fluorescence signals by colloidal silver nanoparticles in studies of protein translation

Metal-enhanced fluorescence (MEF) increased total photon emission of Cy3- and Cy5-labeled ribosomal initiation complexes near 50 nm silver particles 4- and 5.5-fold, respectively. Fluorescence intensity fluctuations above shot noise, at 0.1-5 Hz, were greater on silver particles. Overall signal-to-noise ratio was similar or slightly improved near the particles. Proximity to silver particles did not compromise ribosome function, as measured by codon-dependent binding of fluorescent tRNA, dynamics of fluorescence resonance energy transfer between adjacent tRNAs in the ribosome, and tRNA translocation induced by elongation factor G.

Taming free energy landscapes with RNA chaperones

Many non-coding RNAs fold into complex three-dimensional structures, yet the self-assembly of RNA structure is hampered by mispairing, weak tertiary interactions, electrostatic barriers, and the frequent requirement that the 5' and 3' ends of the transcript interact. This rugged free energy landscape for RNA folding means that some RNA molecules in a population rapidly form their native structure, while many others become kinetically trapped in misfolded conformations. Transient binding of RNA chaperone proteins destabilize misfolded intermediates and lower the transition states between conformations, producing a smoother landscape that increases the rate of folding and the probability that a molecule will find the native structure. DEAD-box proteins couple the chemical potential of ATP hydrolysis with repetitive cycles of RNA binding and release, expanding the range of conditions under which they can refold RNA structures.

Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization

Single-molecule fluorescence spectroscopy reveals the real time dynamics that occur during biomolecular interactions that would otherwise be hidden by the ensemble average. It also removes the requirement to synchronize reactions, thus providing a very intuitive approach to study kinetics of biological systems. Surface immobilization is commonly used to increase observation times to the minute time scale, but it can be detrimental if the sample interacts non-specifically with the surface. Here, we review detailed protocols to prevent such interactions by passivating the surface or by trapping the molecules inside surface immobilized lipid vesicles. Finally, we discuss recent examples where these methods were applied to study the dynamics of important cellular processes at the single-molecule level.

Multicolor single-molecule FRET to explore protein folding and binding

Proper protein function in cells, tissues and organisms depends critically on correct protein folding or interaction with partners. Over the last decade, single-molecule FRET (smFRET) has emerged as a powerful tool to probe complex distributions, dynamics, pathways and landscapes in protein folding and binding reactions, leveraging its ability to avoid averaging over an ensemble of molecules. While smFRET was practiced in a two-color form until recently, the last few years have seen the development of enhanced multicolor smFRET methods that provide additional structural information permitting us to probe more complex mechanisms. In this review, we provide a brief introduction to the smFRET technique, then follow with advanced multicolor measurements and end with ongoing methodology developments in microfluidics and protein labeling that are beginning to make these techniques more broadly applicable to answering a number of key questions about folding and binding.

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment.

Many non-coding genes exert their function via an RNA structure which starts emerging while the RNA sequence is being transcribed from the genome. The resulting folding pathway is known to depend on a variety of features such as the transcription speed, the concentration of various ions and the binding of proteins and other molecules. Not all of these influences can be adequately captured by the existing computational methods which try to replicate what happens in vivo. So far, it has been challenging to experimentally investigate co-transcriptional folding pathways in vivo and only little data from in vitro experiments exists. In order to investigate if functionally similar RNA sequences from different organisms fold in a similar way, we have developed a new computational method, called Transat, which does not require the detailed computational modeling of the cellular environment. We show in a comprehensive analysis that our method is capable of detecting known structural features and provide evidence that structural features of the in vivo folding pathways have been conserved for several biologically interesting classes of RNA sequences.

Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics

Studies of the kinetics of biochemical reactions, especially of folding of proteins and RNA, are important for understanding the function of biomolecules and processes in live cells. Many biochemical reactions occur rapidly and thus need to be triggered on very short time scales for their kinetics to be studied, which is often accomplished by mixing in a turbulent flow. More rapid and sample-efficient mixing is achieved in laminar flow in a microfluidic device, in which the sample is two-dimensionally (2D) focused to a thin sheet. Here we describe the design and operation of an ultrafast microfluidic mixer with three-dimensional (3D) flow focusing. The confinement of a 3D-focused sample to a narrow stream near the middle of a microchannel renders its velocity nearly uniform and makes it possible to monitor the reaction kinetics without exclusion of any parts of the sample. Hence, the sample consumption is substantially reduced and the fluorescence of the sample can be monitored without a confocal setup. Moreover, the 3D-focusing allows facile measurements of velocity of the sample with a high spatial resolution using a specially developed technique based on epi-fluorescence imaging. The data on the velocity vs. position are used to precisely calibrate the conversion between position and the reaction time, which is essential for accurate kinetic measurements. The device performs mixing on a 10 micros scale, which is comparable to that of the laminar mixers with 2D focusing. Unlike previous ultrafast laminar mixers, which were machined in hard materials, the present microfluidic device is made of a single cast of poly(dimethylsiloxane), PDMS, and is thus simpler and less expensive to manufacture.

RNA looping by PTB: Evidence using FRET and NMR spectroscopy for a role in splicing repression

Alternative splicing plays an important role in generating proteome diversity. The polypyrimidine tract-binding protein (PTB) is a key alternative splicing factor involved in exon repression. It has been proposed that PTB acts by looping out exons flanked by pyrimidine tracts. We present fluorescence, NMR, and in vivo splicing data in support of a role of PTB in inducing RNA loops. We show that the RNA recognition motifs (RRMs) 3 and 4 of PTB can bind two distant pyrimidine tracts and bring their 5' and 3' ends in close proximity, thus looping the RNA. Efficient looping requires an intervening sequence of 15 nucleotides or longer between the pyrimidine tracts. RRM3 and RRM4 bind the 5' and the 3' pyrimidine tracts, respectively, in a specific directionality and work synergistically for efficient splicing repression in vivo.

Covalent-bond-based immobilization approaches for single-molecule fluorescence

INH: We report two new approaches, using click-chemistry and disulfide bond bridges, to surface-immobilize nucleic acids for single-molecule fluorescence experiments using covalent bonds and self-assembled monolayers. Both approaches are specific and yield comparable results to the avidin-biotin linkage, but offer new surface chemical properties that might be advantageous to prevent non-specific binding of biopolymers to the surface and to expand the range of fluorescent probes that can be employed in single-molecule studies.

Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution

The catalytic mechanism of DNA polymerases involves multiple steps that precede and follow the transfer of a nucleotide to the 3'-hydroxyl of the growing DNA chain. Here we report a single-molecule approach to monitor the movement of E. coli DNA polymerase I (Klenow fragment) on a DNA template during DNA synthesis with single base-pair resolution. As each nucleotide is incorporated, the single-molecule Förster resonance energy transfer intensity drops in discrete steps to values consistent with single-nucleotide incorporations. Purines and pyrimidines are incorporated with comparable rates. A mismatched primer/template junction exhibits dynamics consistent with the primer moving into the exonuclease domain, which was used to determine the fraction of primer-termini bound to the exonuclease and polymerase sites. Most interestingly, we observe a structural change after the incorporation of a correctly paired nucleotide, consistent with transient movement of the polymerase past the preinsertion site or a conformational change in the polymerase. This may represent a previously unobserved step in the mechanism of DNA synthesis that could be part of the proofreading process.

Modulating RNA structure and catalysis: lessons from small cleaving ribozymes

RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.

Single-molecule analysis of protein-free U2-U6 snRNAs

Spliceosomes catalyze the maturation of precursor mRNAs from yeast to humans. Their catalytic core comprises three small nuclear RNAs (U2, U5 and U6) involved in substrate positioning and catalysis. It has been postulated, but never shown experimentally, that the U2/U6 complex adopts at least two conformations that reflect different activation states. We have used single-molecule fluorescence to probe the structural dynamics of a protein-free RNA complex modeling U2/U6 from yeast and mutants of highly conserved regions. Our data show the presence of at least three distinct conformations in equilibrium. The minimal folding pathway consists of a two-step process with an obligatory intermediate. The first step is strongly magnesium dependent and we provide evidence suggesting the second corresponds to the formation of the genetically conserved helix IB. Site-specific mutations in the highly conserved AGC triad and the U80 base in U6 suggest that the observed conformational dynamics correlate with residues that play an important role in splicing.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.

Single-Molecule Fluorescence Studies of RNA: A Decade's Progress

Over the past decade, single-molecule fluorescence studies have elucidated the structure-function relationship of RNA molecules. The real-time observation of individual RNAs by single-molecule fluorescence has unveiled the dynamic behavior of complex RNA systems in unprecedented detail, revealing the presence of transient intermediate states and their kinetic pathways. This review provides an overview of how single-molecule fluorescence has been used to explore the dynamics of RNA folding and catalysis.

Direct single-molecule observation of a protein living in two opposed native structures

Biological activity in proteins requires them to share the energy landscape for folding and global conformational motions, 2 key determinants of function. Although most structural studies to date have focused on fluctuations around a single structural basin, we directly observe the coexistence of 2 symmetrically opposed conformations for a mutant of the Rop-homodimer (Repressor of Primer) in single-molecule fluorescence resonance energy transfer (smFRET) measurements. We find that mild denaturing conditions can affect the sensitive balance between the conformations, generating an equilibrium ensemble consisting of 2 equally occupied structural basins. Despite the need for large-scale conformational rearrangement, both native structures are dynamically and reversibly adopted for the same paired molecules without separation of the constituent monomers. Such an ability of some proteins or protein complexes to switch between conformations by thermal fluctuations and/or minor environmental changes could be central to their ability to control biological function.

RNA folding during transcription: protocols and studies

RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include the 5'- to 3'-polarity of RNA, the transcriptional speed, pausing properties of the RNA polymerase, the effect of the transcriptional complex and associated factors, and the effect of RNA-binding proteins. Identifying strategic pause sites can reveal insights on the folding pathway of the nascent transcript. Structural mapping of the paused transcription complexes identifies important folding intermediates along these pathways. Oligohybridization assays and the appearance of the catalytic activity of a ribozyme either in trans or in cis can be used to monitor cotranscriptional folding under a wide range of conditions. In our laboratory, these methodologies have been applied to study the folding of three highly conserved RNAs (RNase P, SRP, and tmRNA), several circularly permuted forms of a bacterial RNase P RNA, a riboswitch (thiM), and an aptamer-activated ribozyme (glmS).

The structure and folding of branched RNA analyzed by fluorescence resonance energy transfer

Fluorescence resonance energy transfer (FRET) is a spectroscopic means of obtaining distance information over a range up to ~80Å in solution. It is based on the dipolar coupling between the electronic transition moments of a donor and acceptor fluorophore attached at known positions on the RNA species of interest. It can be applied in ensembles of molecules, either by steady-state fluorescence or by lifetime measurements, but it is also very appropriate for single-molecule studies. In addition to the provision of distance information, recent studies have emphasized the orientation dependence of energy transfer.